Simulating the molecular dynamics (MD) using classical or semi-classical trajectories provides important details for the understanding of many chemical reactions, protein folding, drug design, and solvation effects. MD simulations using trajectories have achieved great successes in the computer simulations of various systems, but it is difficult to incorporate quantum effects in a robust way. Therefore, improving quantum wavepacket dynamics and incorporating nonadiabatic transitions and quantum effects into classical and semi-classical molecular dynamics is critical as well as challenging. In this paper, we present a MD scheme in which a new set of equations of motion (EOM) are proposed to effectively propagate nuclear trajectories while conserving quantum mechanical energy which is critical for describing quantum effects like tunneling. The new quantum EOM is tested on a one-state one-dimensional and a two-state two-dimensional model nonadiabatic systems. The global quantum force experienced by each trajectory promotes energy redistribution among the bundle of trajectories, and thus helps the individual trajectory tunnel through the potential barrier higher than the energy of the trajectory itself. Construction of the new quantum force and EOM also provides a better way to treat the issue of back-reaction in mixed quantum-classical (MQC) methods, i.e. self-consistency between quantum degrees of freedom (DOF) and classical DOF.